Starting qr.refine on Sun May 19 19:58:24 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgj_40457.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgj_40457.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=refine restraints=qm engine=aimnet2 clustering=false minimizer=lbfgsb max_bond_rmsd=0.0001 gradient_only=false Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgj_40457.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgj_40457.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgj_40457.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8sgj_40457.map" } cluster { clustering = false } quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { max_bond_rmsd = 0.0001 minimizer = lbfgs *lbfgsb } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = False debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = True cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 10 clustering_method = gnc *bcc altloc_method = average *subtract save_clusters = True bond_with_altloc = True re_calculate_rmsd_tolerance = 0.5 } restraints = cctbx *qm expansion = False quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server basis = Auto charge = None method = Auto memory = None nproc = 1 server_url = "http://127.0.0.1:8000" qm_addon = gcp dftd3 gcp-d3 qm_addon_method = None } refine { dry_run = False sf_algorithm = *direct fft refinement_target_name = *ml ls_wunit_k1 mode = opt *refine gtest number_of_macro_cycles = 1 number_of_weight_search_cycles = 50 number_of_refine_cycles = 5 number_of_micro_cycles = 50 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 50 max_iterations_refine = 50 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = False refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.0001 max_angle_rmsd = 1.7 stop_one_found_first_good_weight = True max_r_work_r_free_gap = 5 r_tolerance = 0.001 rmsd_tolerance = 0.01 opt_log = False pre_opt = False pre_opt_stpmax = 0.1 pre_opt_iter = 10 pre_opt_switch = 2 pre_opt_gconv = 3000 minimizer = lbfgs *lbfgsb shift_evaluation = max *mean } parallel { method = *multiprocessing slurm pbs sge lsf threading nproc = 1 qsub_command = None } output_file_name_prefix = None output_folder_name = "pdb" rst_file = None dump_gradients = None output { filename = None file_name = None prefix = None suffix = None serial = 0 serial_format = "%03d" target_output_format = None *pdb mmcif overwrite = False } ------------------------------------------------------------------------------- Extracting model **************** Symmetric amino acids flipped Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 15271 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 11821 Inner-chain residues flagged as termini: ['pdbres="PRO A 248 "', 'pdbres="PRO A 370 "', 'pdbres="SER A 467 "', 'pdbres="THR A 482 "', 'pdbres="ALA A 644 "', 'pdbres="PRO A 652 "', 'pdbres="THR A 698 "', 'pdbres="ASN A 707 "', 'pdbres="THR A 718 "', 'pdbres="SER A 737 "'] Classifications: {'peptide': 751} Modifications used: {'COO': 6, 'NH2': 2, 'NH3': 4} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 724} Chain breaks: 5 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1609 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1841 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 1.71, per 1000 atoms: 0.11 Number of scatterers: 15271 At special positions: 0 Unit cell: (98.77, 100.43, 146.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 O 1444 8.00 N 1242 7.00 C 4953 6.00 H 7601 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 7590 1.14 - 1.31: 1261 1.31 - 1.48: 3246 1.48 - 1.64: 3308 1.64 - 1.81: 45 Bond restraints: 15450 Sorted by residual: bond pdb=" C PRO A 758 " pdb=" O PRO A 758 " ideal model delta sigma weight residual 1.231 1.248 -0.017 2.00e-02 2.50e+03 6.87e-01 bond pdb=" C PHE A 207 " pdb=" O PHE A 207 " ideal model delta sigma weight residual 1.231 1.247 -0.016 2.00e-02 2.50e+03 6.67e-01 bond pdb=" C VAL A 155 " pdb=" O VAL A 155 " ideal model delta sigma weight residual 1.231 1.247 -0.016 2.00e-02 2.50e+03 6.64e-01 bond pdb=" C LEU A 26 " pdb=" N PRO A 27 " ideal model delta sigma weight residual 1.341 1.328 0.013 1.60e-02 3.91e+03 6.59e-01 bond pdb=" CA PRO A 758 " pdb=" C PRO A 758 " ideal model delta sigma weight residual 1.525 1.508 0.017 2.10e-02 2.27e+03 6.34e-01 ... (remaining 15445 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 180 106.34 - 113.25: 18018 113.25 - 120.17: 4851 120.17 - 127.08: 4740 127.08 - 133.99: 89 Bond angle restraints: 27878 Sorted by residual: angle pdb=" C GLY L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.70 129.54 -7.84 1.80e+00 3.09e-01 1.90e+01 angle pdb=" C ILE A 636 " pdb=" N LEU A 637 " pdb=" CA LEU A 637 " ideal model delta sigma weight residual 121.70 127.64 -5.94 1.80e+00 3.09e-01 1.09e+01 angle pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 116.90 121.42 -4.52 1.50e+00 4.44e-01 9.08e+00 angle pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " ideal model delta sigma weight residual 116.90 120.99 -4.09 1.50e+00 4.44e-01 7.45e+00 angle pdb=" C TYR L 93 " pdb=" CA TYR L 93 " pdb=" CB TYR L 93 " ideal model delta sigma weight residual 110.10 114.25 -4.15 1.90e+00 2.77e-01 4.77e+00 ... (remaining 27873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 6629 15.67 - 31.34: 424 31.34 - 47.00: 152 47.00 - 62.67: 74 62.67 - 78.34: 12 Dihedral angle restraints: 7291 sinusoidal: 3858 harmonic: 3433 Sorted by residual: dihedral pdb=" CA TYR H 60 " pdb=" C TYR H 60 " pdb=" N THR H 61 " pdb=" CA THR H 61 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LEU A 637 " pdb=" C LEU A 637 " pdb=" N SER A 638 " pdb=" CA SER A 638 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.52e+00 dihedral pdb=" CB LYS A 909 " pdb=" CG LYS A 909 " pdb=" CD LYS A 909 " pdb=" CE LYS A 909 " ideal model delta sinusoidal sigma weight residual -180.00 -125.72 -54.28 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 7288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 724 0.029 - 0.057: 329 0.057 - 0.086: 82 0.086 - 0.114: 54 0.114 - 0.142: 28 Chirality restraints: 1217 Sorted by residual: chirality pdb=" CA ILE A 520 " pdb=" N ILE A 520 " pdb=" C ILE A 520 " pdb=" CB ILE A 520 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA VAL A 430 " pdb=" N VAL A 430 " pdb=" C VAL A 430 " pdb=" CB VAL A 430 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 1214 not shown) Planarity restraints: 2283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 133 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 111 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 112 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 52 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO H 53 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " -0.019 5.00e-02 4.00e+02 ... (remaining 2280 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 873 2.06 - 2.70: 22011 2.70 - 3.33: 44080 3.33 - 3.97: 60211 3.97 - 4.60: 88390 Nonbonded interactions: 215565 Sorted by model distance: nonbonded pdb=" OD1 ASP A 408 " pdb=" HG1 THR A 428 " model vdw 1.429 1.800 nonbonded pdb=" OE1 GLN H 35 " pdb=" HE1 TRP H 47 " model vdw 1.526 1.800 nonbonded pdb="HH21 ARG A 396 " pdb=" O ASP A 435 " model vdw 1.532 1.800 nonbonded pdb=" O PHE A 613 " pdb=" H ILE A 641 " model vdw 1.534 1.800 nonbonded pdb="HD21 ASN A 534 " pdb=" OE1 GLN A 563 " model vdw 1.537 1.800 ... (remaining 215560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 31 15.96 2 O 1444 7.97 2 N 1242 6.97 2 C 4953 5.97 2 H 7601 1.00 3 sf(0) = scattering factor at diffraction angle 0. Setting QM defaults Setting QM method to HF Setting QM basis to 6-31g GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.004 0.023 7849 Z= 0.182 ANGLE : 0.904 7.839 10661 Z= 0.433 CHIRALITY : 0.042 0.142 1217 PLANARITY : 0.004 0.045 1340 DIHEDRAL : 11.934 78.340 2758 MIN NONBONDED DISTANCE : 2.060 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.70 RAMACHANDRAN PLOT: OUTLIERS : 0.10 % ALLOWED : 3.21 % FAVORED : 96.69 % ROTAMER: OUTLIERS : 0.12 % ALLOWED : 0.97 % FAVORED : 98.91 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 6.45 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -0.33 (0.25), RESIDUES: 966 HELIX: 0.03 (0.25), RESIDUES: 341 SHEET: 0.02 (0.29), RESIDUES: 303 LOOP : -0.47 (0.34), RESIDUES: 322 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.000 ARG A 532 TYR 0.011 0.001 TYR H 60 PHE 0.011 0.001 PHE A 925 TRP 0.008 0.001 TRP H 33 HIS 0.002 0.001 HIS A 630 Resolution of map is: 3.5056 Map-model correlation coefficient (CC) CC_mask : 0.8391 weight= None bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 Initial weight estimate from ratio of grad norms: 0.20382844374784764 cycle: 0 start: weight= 0.2038 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.2038 bond: 0.023 angle: 2.25 clash: 7.3 rota: 1.69 rama: f: 91.61 o: 0.52 Z: -4.92 cb: 0.78 shift=0.4210 cc_mask=0.8817 cycle: 1 start: weight= 0.1427 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.1427 bond: 0.019 angle: 1.95 clash: 3.3 rota: 0.60 rama: f: 94.41 o: 0.10 Z: -3.95 cb: 0.33 shift=0.3755 cc_mask=0.8766 cycle: 2 start: weight= 0.0999 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.0999 bond: 0.015 angle: 1.76 clash: 1.8 rota: 0.24 rama: f: 95.86 o: 0.10 Z: -3.18 cb: 0.22 shift=0.3399 cc_mask=0.8718 cycle: 3 start: weight= 0.0499 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.0499 bond: 0.012 angle: 1.58 clash: 0.8 rota: 0.24 rama: f: 97.10 o: 0.00 Z: -1.98 cb: 0.11 shift=0.2756 cc_mask=0.8627 cycle: 4 start: weight= 0.0350 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.0350 bond: 0.011 angle: 1.54 clash: 0.6 rota: 0.24 rama: f: 97.20 o: 0.00 Z: -1.63 cb: 0.11 shift=0.2493 cc_mask=0.8581 cycle: 5 start: weight= 0.0245 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.0245 bond: 0.010 angle: 1.52 clash: 0.3 rota: 0.24 rama: f: 97.10 o: 0.00 Z: -1.41 cb: 0.11 shift=0.2305 cc_mask=0.8536 cycle: 6 start: weight= 0.0122 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.0122 bond: 0.009 angle: 1.51 clash: 0.3 rota: 0.36 rama: f: 97.20 o: 0.00 Z: -1.12 cb: 0.11 shift=0.2124 cc_mask=0.8468 cycle: 7 start: weight= 0.0086 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.0086 bond: 0.009 angle: 1.50 clash: 0.3 rota: 0.36 rama: f: 97.20 o: 0.00 Z: -1.05 cb: 0.11 shift=0.2091 cc_mask=0.8443 cycle: 8 start: weight= 0.0060 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.0060 bond: 0.009 angle: 1.50 clash: 0.2 rota: 0.24 rama: f: 97.31 o: 0.00 Z: -1.01 cb: 0.11 shift=0.2061 cc_mask=0.8423 cycle: 9 start: weight= 0.0030 bond: 0.004 angle: 0.90 clash: 1.7 rota: 0.12 rama: f: 96.69 o: 0.10 Z: -0.33 cb: 0.00 shift=0.0000 cc_mask=0.8391 final: weight= 0.0030 bond: 0.009 angle: 1.50 clash: 0.2 rota: 0.24 rama: f: 97.10 o: 0.00 Z: -0.88 cb: 0.11 shift=0.2030 cc_mask=0.8400 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0029975265723113168 start: weight= 0.0030 bond: 0.009 angle: 1.50 clash: 0.2 rota: 0.24 rama: f: 97.10 o: 0.00 Z: -0.88 cb: 0.11 shift=0.0000 cc_mask=0.8391 final: weight= 0.0030 bond: 0.009 angle: 1.50 clash: 0.2 rota: 0.24 rama: f: 97.10 o: 0.00 Z: -0.89 cb: 0.11 shift=0.2051 cc_mask=0.8399 start: weight= 0.0030 bond: 0.009 angle: 1.50 clash: 0.2 rota: 0.24 rama: f: 97.10 o: 0.00 Z: -0.89 cb: 0.11 shift=0.2051 cc_mask=0.8399 final: weight= 0.0030 bond: 0.009 angle: 1.47 clash: 0.4 rota: 0.24 rama: f: 97.62 o: 0.10 Z: -0.98 cb: 0.11 shift=0.2674 cc_mask=0.8386 start: weight= 0.0030 bond: 0.009 angle: 1.47 clash: 0.4 rota: 0.24 rama: f: 97.62 o: 0.10 Z: -0.98 cb: 0.11 shift=0.2674 cc_mask=0.8386 final: weight= 0.0030 bond: 0.009 angle: 1.50 clash: 0.5 rota: 0.36 rama: f: 97.72 o: 0.10 Z: -1.12 cb: 0.11 shift=0.3188 cc_mask=0.8367 start: weight= 0.0030 bond: 0.009 angle: 1.50 clash: 0.5 rota: 0.36 rama: f: 97.72 o: 0.10 Z: -1.12 cb: 0.11 shift=0.3188 cc_mask=0.8367 final: weight= 0.0030 bond: 0.009 angle: 1.49 clash: 0.5 rota: 0.36 rama: f: 97.62 o: 0.10 Z: -1.18 cb: 0.11 shift=0.3492 cc_mask=0.8352 start: weight= 0.0030 bond: 0.009 angle: 1.49 clash: 0.5 rota: 0.36 rama: f: 97.62 o: 0.10 Z: -1.18 cb: 0.11 shift=0.3492 cc_mask=0.8352 final: weight= 0.0030 bond: 0.009 angle: 1.50 clash: 0.5 rota: 0.36 rama: f: 97.52 o: 0.10 Z: -1.24 cb: 0.11 shift=0.3804 cc_mask=0.8336 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.043 7849 Z= 0.470 ANGLE : 1.497 9.460 10661 Z= 0.788 CHIRALITY : 0.105 0.420 1217 PLANARITY : 0.013 0.177 1340 DIHEDRAL : 12.580 130.893 2758 MIN NONBONDED DISTANCE : 2.583 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.52 RAMACHANDRAN PLOT: OUTLIERS : 0.10 % ALLOWED : 2.38 % FAVORED : 97.52 % ROTAMER: OUTLIERS : 0.36 % ALLOWED : 1.33 % FAVORED : 98.31 % CBETA DEVIATIONS : 0.11 % PEPTIDE PLANE: CIS-PROLINE : 6.45 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -1.24 (0.24), RESIDUES: 966 HELIX: -0.67 (0.24), RESIDUES: 329 SHEET: -1.18 (0.27), RESIDUES: 306 LOOP : -0.20 (0.32), RESIDUES: 331 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.019 0.004 ARG A 661 TYR 0.130 0.017 TYR A 180 PHE 0.053 0.010 PHE A 505 TRP 0.100 0.014 TRP H 99 HIS 0.006 0.001 HIS A 744 Resolution of map is: 3.5056 Map-model correlation coefficient (CC) CC_mask : 0.8336 =============================================================================== Job complete usr+sys time: 2217.44 seconds wall clock time: 27 minutes 27.79 seconds (1647.79 seconds total) /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/ase/__init__.py:21: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(np.__version__) < '1.9': /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. other = LooseVersion(other)